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Running titan-nf

TLDR - Quick Start

Step 1, create FOFN, Step 2, run titan-nf, Step 3, that's it!

titan-gc-prepare.py <YOUR_FASTQS> <YOUR_WORKFLOW> <YOUR_PRIMERS> --tsv > samples.txt
titan-nf --samples samples.txt --run_name <YOUR_RUN_NAME>
  • <YOUR_FASTQS>: the directory where your FASTQS are stored
  • <YOUR_WORKFLOW>: the workflow to execute (clearlabs, illumina_pe, illumina_se, or ont)
  • <YOUR_PRIMERS>: the file with your primers in BED format
  • <YOUR_RUN_NAME>: the name of the sequencing run

On the otherhand, if you want to learn more about the process for running titan-nf please keep reading!

Check /opt/titan/data for primers

Some of the common primers used for SARS-CoV-2 seqeuncing are available in /opt/titan/data/

Please make <YOUR_RUN_NAME> informative

It's very important for downstream back up that your run names are informative and unique. If in doubt use the name given to the run before sequencing.

Run titan-nf

With your handy dandy FOFN, you have everything you need to run your samples though titan-nf.

titan-nf --samples samples.txt --run_name test_run
N E X T F L O W  ~  version 21.04.0
Launching `/home/robert_petit/repos/titan-nf/main.nf` [gigantic_legentil] - revision: 69419d039a
executor >  local (3)
[d8/628d96] process > update_pangolin [100%] 1 of 1 ✔
[fc/a123a2] process > titan_gc (test) [100%] 1 of 1 ✔
[a3/e6f0a1] process > merge_results   [100%] 1 of 1 ✔

    Titan-NF Execution Summary
    ---------------------------
    Command Line    : nextflow run /home/robert_petit/repos/titan-nf/main.nf --samples samples.txt --run_name test_run
    Resumed         : true
    Completed At    : 2021-08-05T21:02:36.953970Z
    Duration        : 4m 12s
    Success         : true
    Exit Code       : 0
    Error Report    : -
    Launch Dir      : /home/robert_petit/repos/titan-nf/test
    Working Dir     : /home/robert_petit/repos/titan-nf/test/work

Deleting 'work' directory (Total size was 2.062G)
Completed at: 05-Aug-2021 21:02:37
Duration    : 4m 13s
CPU hours   : 0.3
Succeeded   : 4

And, we're all set (hopefully for you too!) This will leave you with lots out outputs. To learn more about the outputs, please check out the Output Overview.

titan-nf Parameters

Required Parameters:
    --samples FILE          File produced by titan-prepare.py (--tsv used)

    --run_name STR          Name to use for the results folder

Optional Parameters:
    --titan_opts FILE       A JSON file with Titan GC parameters to use.
                                Default: Use Titan-GC's defaults

    --pangolin_docker STR   The pangolin docker image to use
                                Default: Use Titan-GC's defaults

    --profile STR           Profile for Titan GC to use
                                Options: docker or singularity
                                Default: singularity

    --singularity_cache STR
                            Location where Singularity images are saved to
                                Default: /opt/singularity/cache/titan/

    --outdir DIR            Directory to write results to
                                Default: ./

    --max_retry INT         Maximum number of times to retry a failed job
                                Default: 5

    --keep_files            Prevent removal of the "work" directory after
                                a successful run.